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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 851))

Abstract

Cytochrome P450 3A4 (CYP3A4) is the major and most important drug-metabolizing enzyme in humans that oxidizes and clears over a half of all administered pharmaceuticals. This is possible because CYP3A4 is promiscuous with respect to substrate binding and has the ability to catalyze diverse oxidative chemistries in addition to traditional hydroxylation reactions. Furthermore, CYP3A4 binds and oxidizes a number of substrates in a cooperative manner and can be both induced and inactivated by drugs. In vivo, CYP3A4 inhibition could lead to undesired drug-drug interactions and drug toxicity, a major reason for late-stage clinical failures and withdrawal of marketed pharmaceuticals. Owing to its central role in drug metabolism, many aspects of CYP3A4 catalysis have been extensively studied by various techniques. Here, we give an overview of experimental and theoretical methods currently used for investigation and prediction of CYP3A4-ligand interactions, a defining factor in drug metabolism, with an emphasis on the problems addressed and conclusions derived from the studies.

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Notes

  1. 1.

    Abbreviations: ANF α-naphthoflavone, BEC bromoergocryptine, BFC 7-benzyloxy-4-trifluoromethylcoumarin, BQ 7-benzyloxyquinoline, b5 cytochrome b 5, CPR NADPH-cytochrome P450 oxidoreductase, CYP or P450 cytochrome P450.

  2. 2.

    A review of this scope cannot include all the references pertaining to the subject matter.

References

  1. Rendic S, Di Carlo FJ (1997) Human cytochrome P450 enzymes: a status report summarizing their reactions, substrates, inducers, and inhibitors. Drug Metab Rev 29:413–580

    Article  CAS  PubMed  Google Scholar 

  2. Atkins WM, Wang RW, Lu AY (2001) Allosteric behavior in cytochrome P450-dependent in vitro drug-drug interactions: a prospective based on conformational dynamics. Chem Res Toxicol 14:338–347

    Article  CAS  PubMed  Google Scholar 

  3. Hutzler JM, Tracy TS (2002) Atypical kinetic profiles in drug metabolism reactions. Drug Metab Dispos 30:355–362

    Article  CAS  PubMed  Google Scholar 

  4. Atkins WM (2005) Non-Michaelis-Menten kinetics in cytochrome P450-catalyzed reactions. Annu Rev Pharmacol Toxicol 45:291–310

    Article  CAS  PubMed  Google Scholar 

  5. Sligar SG, Denisov IG (2007) Understanding cooperativity in human P450 mediated drug-drug interactions. Drug Metab Rev 39:567–579

    Article  CAS  PubMed  Google Scholar 

  6. Davydov DR, Halpert JR (2008) Allosteric P450 mechanisms: multiple binding sites, multiple conformers or both? Expert Opin Drug Metab Toxicol 4:1523–1535

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Denisov IG, Sligar SG (2012) A novel type of allosteric regulation: functional cooperativity in monomeric proteins. Arch Biochem Biophys 519:91–102

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Jefcoate CR (1978) Measurement of substrate and inhibitor binding to microsomal cytochrome P-450 by optical-difference spectroscopy. Methods Enzymol 52:258–279

    CAS  PubMed  Google Scholar 

  9. Schenkman JB, Sligar SG, Cinti DL (1981) Substrate interaction with cytochrome P-450. Pharmacol Ther 12:43–71

    Article  CAS  PubMed  Google Scholar 

  10. Harlow GR, Halpert JR (1998) Analysis of human cytochrome P450 3A4 cooperativity: construction and characterization of a site-directed mutant that displays hyperbolic steroid hydroxylation kinetics. Proc Natl Acad Sci U S A 95:6636–6641

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Hosea NA, Miller GP, Guengerich FP (2000) Elucidation of distinct ligand binding sites for cytochrome P450 3A4. Biochemistry 39:5929–5939

    Article  CAS  PubMed  Google Scholar 

  12. Ueng YF, Kuwabara T, Chun YJ, Guengerich FP (1997) Cooperativity in oxidations catalyzed by cytochrome P450 3A4. Biochemistry 36:370–381

    Article  CAS  PubMed  Google Scholar 

  13. Roberts AG, Atkins WM (2007) Energetics of heterotropic cooperativity between α-naphthoflavone and testosterone binding to CYP3A4. Arch Biochem Biophys 463:89–101

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Lampe JN, Fernandez C, Nath A, Atkins WM (2008) Nile Red is a fluorescent allosteric substrate of cytochrome P450 3A4. Biochemistry 47:509–516

    Article  CAS  PubMed  Google Scholar 

  15. Cameron MD, Wen B, Roberts AG, Atkins WM, Campbell AP, Nelson SD (2007) Cooperative binding of acetaminophen and caffeine within the P450 3A4 active site. Chem Res Toxicol 20:1434–1441

    Article  CAS  PubMed  Google Scholar 

  16. Maekawa K, Yoshimura T, Saito Y, Fujimura Y, Aohara F, Emoto C, Iwasaki K, Hanioka N, Narimatsu S, Niwa T, Sawada J (2009) Functional characterization of CYP3A4. 16: catalytic activities toward midazolam and carbamazepine. Xenobiotica 39:140–147

    Article  CAS  PubMed  Google Scholar 

  17. Domanski TL, He YA, Khan KK, Roussel F, Wang Q, Halpert JR (2001) Phenylalanine and tryptophan scanning mutagenesis of CYP3A4 substrate recognition site residues and effect on substrate oxidation and cooperativity. Biochemistry 40:10150–10160

    Article  CAS  PubMed  Google Scholar 

  18. Frank DJ, Denisov IG, Sligar SG (2009) Mixing apples and oranges: analysis of heterotropic cooperativity in cytochrome P450 3A4. Arch Biochem Biophys 488:146–152

    Article  CAS  PubMed  Google Scholar 

  19. Denisov IG, Baas BJ, Grinkova YV, Sligar SG (2007) Cooperativity in cytochrome P450 3A4: linkages in substrate binding, spin state, uncoupling, and product formation. J Biol Chem 282:7066–7076

    Article  CAS  PubMed  Google Scholar 

  20. Frank DJ, Denisov IG, Sligar SG (2011) Analysis of heterotropic cooperativity in cytochrome P450 3A4 using α-naphthoflavone and testosterone. J Biol Chem 286:5540–5545

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Roberts AG, Campbell AP, Atkins WM (2005) The thermodynamic landscape of testosterone binding to cytochrome P450 3A4: ligand binding and spin state equilibria. Biochemistry 44:1353–1366

    Article  CAS  PubMed  Google Scholar 

  22. Fernando H, Halpert JR, Davydov DR (2006) Resolution of multiple substrate binding sites in cytochrome P450 3A4: the stoichiometry of the enzyme-substrate complexes probed by FRET and Job’s titration. Biochemistry 45:4199–4209

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Fernando H, Davydov DR, Chin CC, Halpert JR (2007) Role of subunit interactions in P450 oligomers in the loss of homotropic cooperativity in the cytochrome P450 3A4 mutant L211F/D214E/F304W. Arch Biochem Biophys 460:129–140

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Fernando H, Rumfeldt JA, Davydova NY, Halpert JR, Davydov DR (2011) Multiple substrate-binding sites are retained in cytochrome P450 3A4 mutants with decreased cooperativity. Xenobiotica 41:281–289

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Renaud JP, Davydov DR, Heirwegh KP, Mansuy D, Hui Bon Hoa GH (1996) Thermodynamic studies of substrate binding and spin transitions in human cytochrome P-450 3A4 expressed in yeast microsomes. Biochem J 319(Pt 3):675–681

    PubMed Central  CAS  PubMed  Google Scholar 

  26. Isin EM, Guengerich FP (2006) Kinetics and thermodynamics of ligand binding by cytochrome P450 3A4. J Biol Chem 281:9127–9136

    Article  CAS  PubMed  Google Scholar 

  27. Isin EM, Guengerich FP (2007) Multiple sequential steps involved in the binding of inhibitors to cytochrome P450 3A4. J Biol Chem 282:6863–6874

    Article  CAS  PubMed  Google Scholar 

  28. Sevrioukova IF, Poulos TL (2010) Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir. Proc Natl Acad Sci U S A 107:18422–18427

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Sevrioukova IF, Poulos TL (2012) Structural and mechanistic insights into the interaction of cytochrome P4503A4 with bromoergocryptine, a type I ligand. J Biol Chem 287:3510–3517

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Sevrioukova IF, Poulos TL (2012) Interaction of human cytochrome P4503A4 with ritonavir analogs. Arch Biochem Biophys 520:108–116

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Sevrioukova IF, Poulos TL (2013) Pyridine-substituted desoxyritonavir is a more potent cytochrome P450 3A4 inhibitor than ritonavir. J Med Chem 56:3733–3741

    Article  CAS  PubMed  Google Scholar 

  32. Yamazaki H, Ueng YF, Shimada T, Guengerich FP (1995) Roles of divalent metal ions in oxidations catalyzed by recombinant cytochrome P450 3A4 and replacement of NADPH-cytochrome P450 reductase with other flavoproteins, ferredoxin, and oxygen surrogates. Biochemistry 34:8380–8389

    Article  CAS  PubMed  Google Scholar 

  33. Guengerich FP, Johnson WW (1997) Kinetics of ferric cytochrome P450 reduction by NADPH-cytochrome P450 reductase: rapid reduction in the absence of substrate and variations among cytochrome P450 systems. Biochemistry 36:14741–14750

    Article  CAS  PubMed  Google Scholar 

  34. Davydov DR, Fernando H, Baas BJ, Sligar SG, Halpert JR (2005) Kinetics of dithionite-dependent reduction of cytochrome P450 3A4: heterogeneity of the enzyme caused by its oligomerization. Biochemistry 44:13902–13913

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Fernando H, Halpert JR, Davydov DR (2008) Kinetics of electron transfer in the complex of cytochrome P450 3A4 with the flavin domain of cytochrome P450BM-3 as evidence of functional heterogeneity of the heme protein. Arch Biochem Biophys 471:20–31

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Davydov DR, Sineva EV, Sistla S, Davydova NY, Frank DJ, Sligar SG, Halpert JR (2010) Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium. Biochim Biophys Acta 1797:378–390

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Koley AP, Buters JT, Robinson RC, Markowitz A, Friedman FK (1995) CO binding kinetics of human cytochrome P450 3A4. Specific interaction of substrates with kinetically distinguishable conformers. J Biol Chem 270:5014–5018

    Article  CAS  PubMed  Google Scholar 

  38. Koley AP, Robinson RC, Friedman FK (1996) Cytochrome P450 conformation and substrate interactions as probed by CO binding kinetics. Biochimie 78:706–713

    Article  CAS  PubMed  Google Scholar 

  39. Koley AP, Buters JT, Robinson RC, Markowitz A, Friedman FK (1997) Differential mechanisms of cytochrome P450 inhibition and activation by α-naphthoflavone. J Biol Chem 272:3149–3152

    Article  CAS  PubMed  Google Scholar 

  40. Kumar S, Davydov DR, Halpert JR (2005) Role of cytochrome b 5 in modulating peroxide-supported CYP3A4 activity: evidence for a conformational transition and cytochrome P450 heterogeneity. Drug Metab Dispos 33:1131–1136

    Article  CAS  PubMed  Google Scholar 

  41. Davydov DR, Halpert JR, Renaud JP, Hui Bon Hoa G (2003) Conformational heterogeneity of cytochrome P450 3A4 revealed by high pressure spectroscopy. Biochem Biophys Res Commun 312:121–130

    Article  CAS  PubMed  Google Scholar 

  42. Davydov DR, Baas BJ, Sligar SG, Halpert JR (2007) Allosteric mechanisms in cytochrome P450 3A4 studied by high-pressure spectroscopy: pivotal role of substrate-induced changes in the accessibility and degree of hydration of the heme pocket. Biochemistry 46:7852–7864

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. Kapelyukh Y, Paine MJ, Marechal JD, Sutcliffe MJ, Wolf CR, Roberts GC (2008) Multiple substrate binding by cytochrome P450 3A4: estimation of the number of bound substrate molecules. Drug Metab Dispos 36:2136–2144

    Article  CAS  PubMed  Google Scholar 

  44. Dabrowski MJ, Schrag ML, Wienkers LC, Atkins WM (2002) Pyrene-pyrene complexes at the active site of cytochrome P450 3A4: evidence for a multiple substrate binding site. J Am Chem Soc 124:11866–11867

    Article  CAS  PubMed  Google Scholar 

  45. Nath A, Fernandez C, Lampe JN, Atkins WM (2008) Spectral resolution of a second binding site for Nile Red on cytochrome P4503A4. Arch Biochem Biophys 474:198–204

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Davydov DR, Davydova NY, Sineva EV, Kufareva I, Halpert JR (2013) Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone. Biochem J 453:219–230

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Nath A, Koo PK, Rhoades E, Atkins WM (2008) Allosteric effects on substrate dissociation from cytochrome P450 3A4 in nanodiscs observed by ensemble and single-molecule fluorescence spectroscopy. J Am Chem Soc 130:15746–15747

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Stresser DM, Blanchard AP, Turner SD, Erve JC, Dandeneau AA, Miller VP, Crespi CL (2000) Substrate-dependent modulation of CYP3A4 catalytic activity: analysis of 27 test compounds with four fluorometric substrates. Drug Metab Dispos 28:1440–1448

    CAS  PubMed  Google Scholar 

  49. Chougnet A, Grinkova Y, Ricard D, Sligar S, Woggon WD (2007) Fluorescent probes for rapid screening of potential drug-drug interactions at the CYP3A4 level. ChemMedChem 2:717–724

    Article  CAS  PubMed  Google Scholar 

  50. Lampe JN, Atkins WM (2006) Time-resolved fluorescence studies of heterotropic ligand binding to cytochrome P450 3A4. Biochemistry 45:12204–12215

    Article  CAS  PubMed  Google Scholar 

  51. Tsalkova TN, Davydova NY, Halpert JR, Davydov DR (2007) Mechanism of interactions of α-naphthoflavone with cytochrome P450 3A4 explored with an engineered enzyme bearing a fluorescent probe. Biochemistry 46:106–119

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Davydov DR, Davydova NY, Tsalkova TN, Halpert JR (2008) Effect of glutathione on homo- and heterotropic cooperativity in cytochrome P450 3A4. Arch Biochem Biophys 471:134–145

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  53. Gartner CA, Wen B, Wan J, Becker RS, Jones G 2nd, Gygi SP, Nelson SD (2005) Photochromic agents as tools for protein structure study: lapachenole is a photoaffinity ligand of cytochrome P450 3A4. Biochemistry 44:1846–1855

    Article  CAS  PubMed  Google Scholar 

  54. Wen B, Doneanu CE, Gartner CA, Roberts AG, Atkins WM, Nelson SD (2005) Fluorescent photoaffinity labeling of cytochrome P450 3A4 by lapachenole: identification of modification sites by mass spectrometry. Biochemistry 44:1833–1845

    Article  CAS  PubMed  Google Scholar 

  55. Kim JS, Ahn T, Yim SK, Yun CH (2002) Differential effect of copper (II) on the cytochrome P450 enzymes and NADPH-cytochrome P450 reductase: inhibition of cytochrome P450-catalyzed reactions by copper (II) ion. Biochemistry 41:9438–9447

    Article  CAS  PubMed  Google Scholar 

  56. Kim JS, Yun CH (2005) Inhibition of human cytochrome P450 3A4 activity by zinc(II) ion. Toxicol Lett 156:341–350

    Article  CAS  PubMed  Google Scholar 

  57. Baylon JL, Lenov IL, Sligar SG, Tajkhorshid E (2013) Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation. J Am Chem Soc 135:8542–8851

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  58. Pearson JT, Hill JJ, Swank J, Isoherranen N, Kunze KL, Atkins WM (2006) Surface plasmon resonance analysis of antifungal azoles binding to CYP3A4 with kinetic resolution of multiple binding orientations. Biochemistry 45:6341–6353

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  59. Pearson J, Dahal UP, Rock D, Peng CC, Schenk JO, Joswig-Jones C, Jones JP (2011) The kinetic mechanism for cytochrome P450 metabolism of type II binding compounds: evidence supporting direct reduction. Arch Biochem Biophys 511:69–79

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  60. Das A, Zhao J, Schatz GC, Sligar SG, Van Duyne RP (2009) Screening of type I and II drug binding to human cytochrome P450-3A4 in nanodiscs by localized surface plasmon resonance spectroscopy. Anal Chem 81:3754–3759

    Article  CAS  PubMed  Google Scholar 

  61. Cameron MD, Wen B, Allen KE, Roberts AG, Schuman JT, Campbell AP, Kunze KL, Nelson SD (2005) Cooperative binding of midazolam with testosterone and α-naphthoflavone within the CYP3A4 active site: a NMR T1 paramagnetic relaxation study. Biochemistry 44:14143–14151

    Article  CAS  PubMed  Google Scholar 

  62. Roberts AG, Yang J, Halpert JR, Nelson SD, Thummel KT, Atkins WM (2011) The structural basis for homotropic and heterotropic cooperativity of midazolam metabolism by human cytochrome P450 3A4. Biochemistry 50:10804–10818

    Article  CAS  PubMed  Google Scholar 

  63. Kijac AZ, Li Y, Sligar SG, Rienstra CM (2007) Magic-angle spinning solid-state NMR spectroscopy of nanodisc-embedded human CYP3A4. Biochemistry 46:13696–13703

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  64. Conner KP, Vennam P, Woods CM, Krzyaniak MD, Bowman MK, Atkins WM (2012) 1,2,3-Triazole-heme interactions in cytochrome P450: functionally competent triazole-water-heme complexes. Biochemistry 51:6441–6457

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  65. Mak PJ, Denisov IG, Grinkova YV, Sligar SG, Kincaid JR (2011) Defining CYP3A4 structural responses to substrate binding. Raman spectroscopic studies of a nanodisc-incorporated mammalian cytochrome P450. J Am Chem Soc 133:1357–1366

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  66. Obach RS (2001) Mechanism of cytochrome P4503A4- and 2D6-catalyzed dehydrogenation of ezlopitant as probed with isotope effects using five deuterated analogs. Drug Metab Dispos 29:1599–1607

    CAS  PubMed  Google Scholar 

  67. Krauser JA, Guengerich FP (2005) Cytochrome P450 3A4-catalyzed testosterone 6β-hydroxylation stereochemistry, kinetic deuterium isotope effects, and rate-limiting steps. J Biol Chem 280:19496–19506

    Article  CAS  PubMed  Google Scholar 

  68. Woods CM, Fernandez C, Kunze KL, Atkins WM (2011) Allosteric activation of cytochrome P450 3A4 by α-naphthoflavone: branch point regulation revealed by isotope dilution analysis. Biochemistry 50:10041–10051

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  69. Joseph S, Rusling JF, Lvov YM, Friedberg T, Fuhr U (2003) An amperometric biosensor with human CYP3A4 as a novel drug screening tool. Biochem Pharmacol 65:1817–1826

    Article  CAS  PubMed  Google Scholar 

  70. Xue Q, Kato D, Kamata T, Guo Q, You T, Niwa O (2013) Human cytochrome P450 3A4 and a carbon nanofiber modified film electrode as a platform for the simple evaluation of drug metabolism and inhibition reactions. Analyst 138:6463–6468

    Article  CAS  PubMed  Google Scholar 

  71. Sadeghi SJ, Ferrero S, Di Nardo G, Gilardi G (2012) Drug-drug interactions and cooperative effects detected in electrochemically driven human cytochrome P450 3A4. Bioelectrochemistry 86:87–91

    Article  CAS  PubMed  Google Scholar 

  72. Hendricks NR, Waryo TT, Arotiba O, Jahed N, Baker PGL, Iwuoha EI (2009) Microsomal cytochrome P450-3A4 (CYP3A4) nanobiosensor for the determination of 2,4-dichlorophenol − an endocrine disruptor compound. Electrochim Acta 54:1925–1931

    Article  CAS  Google Scholar 

  73. Ignaszak A, Hendricks N, Waryo T, Songa E, Jahed N, Ngece R, Al-Ahmed A, Kgarebe B, Baker P, Iwuoha EI (2009) Novel therapeutic biosensor for indinavir − a protease inhibitor antiretroviral drug. J Pharm Biomed Anal 49:498–501

    Article  CAS  PubMed  Google Scholar 

  74. Mie Y, Suzuki M, Komatsu Y (2009) Electrochemically driven drug metabolism by membranes containing human cytochrome P450. J Am Chem Soc 131:6646–6647

    Article  CAS  PubMed  Google Scholar 

  75. Larsen AT, May EM, Auclair K (2011) Predictable stereoselective and chemoselective hydroxylations and epoxidations with P450 3A4. J Am Chem Soc 133:7853–7858

    Article  CAS  PubMed  Google Scholar 

  76. Johnson EF, Stout CD (2005) Structural diversity of human xenobiotic-metabolizing cytochrome P450 monooxygenases. Biochem Biophys Res Commun 338:331–336

    Article  CAS  PubMed  Google Scholar 

  77. Williams PA, Cosme J, Vinkovic DM, Ward A, Angove HC, Day PJ, Vonrhein C, Tickle IJ, Jhoti H (2004) Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science 305:683–686

    Article  CAS  PubMed  Google Scholar 

  78. Yano JK, Wester MR, Schoch GA, Griffin KJ, Stout CD, Johnson EF (2004) The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-Å resolution. J Biol Chem 279:38091–38094

    Article  CAS  PubMed  Google Scholar 

  79. Ekroos M, Sjogren T (2006) Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci U S A 103:13682–13687

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  80. Sevrioukova IF, Poulos TL (2013) Dissecting cytochrome P450 3A4-ligand interactions using ritonavir analogues. Biochemistry 52:4474–4481

    Article  CAS  PubMed  Google Scholar 

  81. Sevrioukova IF, Poulos TL (2014) Ritonavir analogues as a probe for deciphering the cytochrome P450 3A4 inhibitory mechanism. Curr Topics Med Chem 14:1348–1355

    Google Scholar 

  82. Cupp-Vickery J, Anderson R, Hatziris Z (2000) Crystal structures of ligand complexes of P450eryF exhibiting homotropic cooperativity. Proc Natl Acad Sci U S A 97:3050–3055

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  83. Park H, Lee S, Suh J (2005) Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc 127:13634–13642

    Article  CAS  PubMed  Google Scholar 

  84. Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R (2007) Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4. J Am Chem Soc 129:1602–1611

    Article  CAS  PubMed  Google Scholar 

  85. Sun H, Moore C, Dansette PM, Kumar S, Halpert JR, Yost GS (2009) Dehydrogenation of the indoline-containing drug 4-chloro-N-(2-methyl-1-indolinyl)-3-sulfamoylbenzamide (indapamide) by CYP3A4: correlation with in silico predictions. Drug Metab Dispos 37:672–684

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  86. Sun H, Scott DO (2011) Metabolism of 4-aminopiperidine drugs by cytochrome P450s: molecular and quantum mechanical insights into drug design. ACS Med Chem Lett 2:638–643

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  87. Li W, Liu H, Luo X, Zhu W, Tang Y, Halpert JR, Jiang H (2007) Possible pathway(s) of metyrapone egress from the active site of cytochrome P450 3A4: a molecular dynamics simulation. Drug Metab Dispos 35:689–696

    Article  CAS  PubMed  Google Scholar 

  88. Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R (2009) Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem 113:13018–13025

    Article  CAS  Google Scholar 

  89. Krishnamoorthy N, Gajendrarao P, Thangapandian S, Lee Y, Lee KW (2009) Probing possible egress channels for multiple ligands in human CYP3A4: a molecular modeling study. J Mol Model 16:607–614

    Article  PubMed  CAS  Google Scholar 

  90. Shahrokh K, Cheatham TE 3rd, Yost GS (2012) Conformational dynamics of CYP3A4 demonstrate the important role of Arg212 coupled with the opening of ingress, egress and solvent channels to dehydrogenation of 4-hydroxytamoxifen. Biochim Biophys Acta 1820:1605–1617

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  91. Bren U, Oostenbrink C (2012) Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free- energy calculations. J Chem Inf Model 52:1573–1582

    Article  CAS  PubMed  Google Scholar 

  92. Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R (2010) How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel? J Phys Chem 114:5964–5970

    Article  CAS  Google Scholar 

  93. Denisov IG, Shih AY, Sligar SG (2012) Structural differences between soluble and membrane bound cytochrome P450s. J Inorg Biochem 108:150–158

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  94. Berka K, Paloncyova M, Anzenbacher P, Otyepka M (2013) Behavior of human cytochromes P450 on lipid membranes. J Phys Chem 117:11556–11564

    Article  CAS  Google Scholar 

  95. Liu X, Wang X, Jiang H (2008) A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation. J Biochem Biophys Methods 70:857–864

    Article  CAS  PubMed  Google Scholar 

  96. Yang K, Liu X, Wang X, Jiang H (2009) A steered molecular dynamics method with adaptive direction adjustments. Biochem Biophys Res Commun 379:494–498

    Article  CAS  PubMed  Google Scholar 

  97. Torimoto N, Ishii I, Hata M, Nakamura H, Imada H, Ariyoshi N, Ohmori S, Igarashi T, Kitada M (2003) Direct interaction between substrates and endogenous steroids in the active site may change the activity of cytochrome P450 3A4. Biochemistry 42:15068–15077

    Article  CAS  PubMed  Google Scholar 

  98. Fishelovitch D, Hazan C, Hirao H, Wolfson HJ, Nussinov R, Shaik S (2007) QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. J Phys Chem 111:13822–13832

    Article  CAS  Google Scholar 

  99. Zhang Y, Morisetti P, Kim J, Smith L, Lin H (2008) Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4. Theor Chem Acc 121:313–319

    Article  CAS  Google Scholar 

  100. Kongsted J, Ryde U (2009) An improved method to predict the entropy term with the MM/PBSA approach. J Comput Aided Mol Des 23:63–71

    Article  CAS  PubMed  Google Scholar 

  101. Zhang Y, Lin H (2009) Quantum tunneling in testosterone 6β-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces. J Phys Chem 113:11501–11508

    Article  CAS  Google Scholar 

  102. Lee JY, Kang NS, Kang YK (2012) Binding free energies of inhibitors to iron porphyrin complex as a model for cytochrome P450. Biopolymers 97:219–228

    Article  CAS  PubMed  Google Scholar 

  103. de Groot MJ, Ekins S (2002) Pharmacophore modeling of cytochromes P450. Adv Drug Deliv Rev 54:367–383

    Article  PubMed  Google Scholar 

  104. Wang Y, Han KL, Sheng-Li Y, Yang L (2004) Structural determinants of steroids for cytochrome P450 3A4-mediated metabolism. J Mol Struct 710:215–221

    Article  CAS  Google Scholar 

  105. Ekins S, Bravi G, Wikel JH, Wrighton SA (1999) Three-dimensional-quantitative structure activity relationship analysis of cytochrome P-450 3A4 substrates. J Pharmacol Exp Ther 291:424–433

    CAS  PubMed  Google Scholar 

  106. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH, Wrighton SA (1999) Three- and four-dimensional quantitative structure activity relationship analyses of cytochrome P-450 3A4 inhibitors. J Pharmacol Exp Ther 290:429–438

    CAS  PubMed  Google Scholar 

  107. Riley RJ, Parker AJ, Trigg S, Manners CN (2001) Development of a generalized, quantitative physicochemical model of CYP3A4 inhibition for use in early drug discovery. Pharm Res 18:652–655

    Article  CAS  PubMed  Google Scholar 

  108. Ekins S, Stresser DM, Williams JA (2003) In vitro and pharmacophore insights into CYP3A enzymes. Trends Pharmacol Sci 24:161–166

    Article  CAS  PubMed  Google Scholar 

  109. Ekins S, Berbaum J, Harrison RK (2003) Generation and validation of rapid computational filters for CYP2D6 and CYP3A4. Drug Metab Dispos 31:1077–1080

    Article  CAS  PubMed  Google Scholar 

  110. Regev-Shoshani G, Shoseyov O, Kerem Z (2004) Influence of lipophilicity on the interactions of hydroxy stilbenes with cytochrome P450 3A4. Biochem Biophys Res Commun 323:668–673

    Article  CAS  PubMed  Google Scholar 

  111. Singh SB, Shen LQ, Walker MJ, Sheridan RP (2003) A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules. J Med Chem 46:1330–1336

    Article  CAS  PubMed  Google Scholar 

  112. Mao B, Gozalbes R, Barbosa F, Migeon J, Merrick S, Kamm K, Wong E, Costales C, Shi W, Wu C, Froloff N (2006) QSAR modeling of in vitro inhibition of cytochrome P450 3A4. J Chem Inf Model 46:2125–2134

    Article  CAS  PubMed  Google Scholar 

  113. Lill MA, Dobler M, Vedani A (2006) Prediction of small-molecule binding to cytochrome P450 3A4: flexible docking combined with multidimensional QSAR. Chem Med Chem 1:73–81

    Article  CAS  PubMed  Google Scholar 

  114. Sheridan RP, Korzekwa KR, Torres RA, Walker MJ (2007) Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9. J Med Chem 50:3173–3184

    Article  CAS  PubMed  Google Scholar 

  115. Kjellander B, Masimirembwa CM, Zamora I (2007) Exploration of enzyme-ligand interactions in CYP2D6 and 3A4 homology models and crystal structures using a novel computational approach. J Chem Inf Model 47:1234–1247

    Article  CAS  PubMed  Google Scholar 

  116. Jayakanthan M, Chandrasekar S, Muthukumaran J, Mathur PP (2010) Analysis of CYP3A4-HIV-1 protease drugs interactions by computational methods for highly active antiretroviral therapy in HIV/AIDS. J Mol Graph Model 28:455–463

    Article  CAS  PubMed  Google Scholar 

  117. Dapkunas J, Sazonovas A, Japertas P (2009) Probabilistic prediction of the human CYP3A4 and CYP2D6 metabolism sites. Chem Biodivers 6:2101–2106

    Article  CAS  PubMed  Google Scholar 

  118. Didziapetris R, Dapkunas J, Sazonovas A, Japertas P (2010) Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition. J Comput Aided Mol Des 24:891–906

    Article  CAS  PubMed  Google Scholar 

  119. Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S (2013) Three-dimensional quantitative structure-activity relationship analysis of inhibitors of human and rat cytochrome P4503A enzymes. Drug Metab Pharmacokinet 28:345–355

    Article  CAS  PubMed  Google Scholar 

  120. Tie Y, McPhail B, Hong H, Pearce BA, Schnackenberg LK, Ge W, Buzatu DA, Wilkes JG, Fuscoe JC, Tong W, Fowler BA, Beger RD, Demchuk E (2013) Modeling chemical interaction profiles: II. Molecular docking, spectral data-activity relationship, and structure-activity relationship models for potent and weak inhibitors of cytochrome P450 CYP3A4 isozyme. Molecules 17:3407–3460

    Article  CAS  Google Scholar 

  121. Jensen BF, Vind C, Padkjaer SB, Brockhoff PB, Refsgaard HH (2007) In silico prediction of cytochrome P450 2D6 and 3A4 inhibition using Gaussian kernel weighted k-nearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors. J Med Chem 50:501–511

    Article  CAS  PubMed  Google Scholar 

  122. Zhou D, Afzelius L, Grimm SW, Andersson TB, Zauhar RJ, Zamora I (2006) Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions. Drug Metab Dispos 34:976–983

    CAS  PubMed  Google Scholar 

  123. Vedani A, Dobler M, Lill MA (2006) The challenge of predicting drug toxicity in silico. Basic Clin Pharmacol Toxicol 99:195–208

    Article  CAS  PubMed  Google Scholar 

  124. Sun H, Scott DO (2010) Structure-based drug metabolism predictions for drug design. Chem Biol Drug Des 75:3–17

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

Financial support from the National Institute of General Medical Sciences (Grant GM57353) and the California Center for Antiviral Drug Discovery is gratefully appreciated.

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Correspondence to Irina F. Sevrioukova .

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Sevrioukova, I.F., Poulos, T.L. (2015). Current Approaches for Investigating and Predicting Cytochrome P450 3A4-Ligand Interactions. In: Hrycay, E., Bandiera, S. (eds) Monooxygenase, Peroxidase and Peroxygenase Properties and Mechanisms of Cytochrome P450. Advances in Experimental Medicine and Biology, vol 851. Springer, Cham. https://doi.org/10.1007/978-3-319-16009-2_3

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